Fig. 3: Maximum-likelihood tree of all ATP synthase headpiece subunits identified in sampled Archaea (red), Bacteria (blue), and Eukaryotes (yellow).
From: ATP synthase evolution on a cross-braced dated tree of life
A Homologs corresponding to each subunit form monophyletic clusters for each protein family. Catalytic subunits (cF1 and cA1V1) and non-catalytic subunits (ncF1 and ncA1V1) cluster together on either side of the root. The alignment contains 1520 sequences and was trimmed with BMGE v1.12 (settings: -m BLOSUM30 -h 0.55)110 (alignment length = 350 amino acids). The maximum-likelihood tree was inferred using IQ-TREE2 v2.1.2 with the LG+C50+R+F model, selected using the best-fitting model (chosen by BIC)111,123,132. The scale bar corresponds to the expected number of substitutions per site. The Walker-A motif from ancestrally reconstructed sequences123 are shown at their respective nodes. B Conserved protein motifs for each subunit derived from the same alignment.
